Abstract
WRKY proteins comprise one of the largest transcription factor families in plants and form key regulators of many plant processes. This study presents the characterization of 58 WRKY genes from the castor bean (Ricinus communis L., Euphorbiaceae) genome. Compared with the automatic genome annotation, one more WRKY-encoding locus was identified and 20 out of the 57 predicted gene models were manually corrected. All RcWRKY genes were shown to contain at least one intron in their coding sequences. According to the structural features of the present WRKY domains, the identified RcWRKY genes were assigned to three previously defined groups (I–III). Although castor bean underwent no recent whole-genome duplication event like physic nut (Jatropha curcas L., Euphorbiaceae), comparative genomics analysis indicated that one gene loss, one intron loss and one recent proximal duplication occurred in the RcWRKY gene family. The expression of all 58 RcWRKY genes was supported by ESTs and/or RNA sequencing reads derived from roots, leaves, flowers, seeds and endosperms. Further global expression profiles with RNA sequencing data revealed diverse expression patterns among various tissues. Results obtained from this study not only provide valuable information for future functional analysis and utilization of the castor bean WRKY genes, but also provide a useful reference to investigate the gene family expansion and evolution in Euphorbiaceus plants.
Highlights
WRKY transcription factors, defined by the presence of the conserved WRKY domain of approximate 60 amino acids, play an essential regulatory role in plant growth, development, metabolism, and biotic and abiotic stress responses [1,2,3]
57 loci were predicted by the genome annotation [20] and further annotated by the PlantTFDB which used the released gene models for the annotation of RcWRKY genes [37], whereas one more loci encoding 117 residues was identified from the scaffold28842 (Table 1) and its ortholog was found in physic nut [7]
Since the gene models of RcWRKY genes were the result of an automatic annotation due to the lack of transcriptome data at that time, an expert revision of their gene structures was conducted via mapping the expressed sequence tags (ESTs) and reads against the scaffolds
Summary
WRKY transcription factors, defined by the presence of the conserved WRKY domain of approximate 60 amino acids, play an essential regulatory role in plant growth, development, metabolism, and biotic and abiotic stress responses [1,2,3]. WRKY proteins contain one or two WRKY domains, comprising the highly conserved WRKYGQK heptapeptide at the N-termini and a novel zinc finger motif (Cx4– 7Cx22–23HxH/C) at the C-termini [10]. Both of these two motifs are vital for the high binding affinity of the WRKY proteins to the consensus cis-acting element termed the W box (TTGACT/ C) [15,16]. According to the number of WRKY domains and the features of their zinc finger motifs, WRKY proteins can be categorized into three main groups. The group I members have two WRKY domains and feature the zinc finger motif of C2H2. In contrast to the presence of a conserved PR intron located after the codon encoding arginine (N terminal to the zinc finger motif) of subgroups c-e as seen in the group III and the C-terminal WRKY domain of the group I, members of subgroups a and b harbor a VQR intron in the zinc finger motif instead [6,10,17]
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